Merge pull request #101 from lycosystem/release-1.3.4

Release 1.3.4

Author: rmnldwg

.github/workflows/build.yml

@@ -0,0 +1,56 @@
+name: Build and release Python package on PyPI
+
+on:
+  release:
+    types: [ created ]
+
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build package from source
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: Install Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Install build tools
+        run: |
+          python3 -m pip install build --user
+      - name: Build package
+        run: |
+          python3 -m build
+      - name: Upload to CI runner
+        uses: actions/upload-artifact@v4
+        with:
+          name: built-package
+          path: dist/
+
+  pypi-publish:
+    name: Publish built package on PyPI
+    runs-on: ubuntu-latest
+    needs:
+      - build
+
+    # Specifying a GitHub environment is optional, but strongly encouraged
+    environment:
+      name: pypi
+      url: https://pypi.org/p/lymph-model
+    permissions:
+      # IMPORTANT: this permission is mandatory for Trusted Publishing
+      id-token: write
+    steps:
+      # retrieve your distributions here
+      - name: Download from CI runner
+        uses: actions/download-artifact@v4
+        with:
+          name: built-package
+          path: dist/
+      - name: Publish on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/release.yml

@@ -0,0 +1,59 @@
+name: Build and release Python package on TestPyPI
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+jobs:
+  build:
+    name: Build package from source
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          persist-credentials: false
+          fetch-depth: 0
+      - name: Install Python 3
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - name: Install build tools
+        run: |
+          python3 -m pip install build --user
+      - name: Build package
+        run: |
+          python3 -m build
+      - name: Upload to CI runner
+        uses: actions/upload-artifact@v4
+        with:
+          name: built-package
+          path: dist/
+
+  testpypi-publish:
+    name: Publish built package on TestPyPI
+    runs-on: ubuntu-latest
+    needs:
+      - build
+
+    # Specifying a GitHub environment is optional, but strongly encouraged
+    environment:
+      name: testpypi
+      url: https://test.pypi.org/p/lymph-model
+    permissions:
+      # IMPORTANT: this permission is mandatory for Trusted Publishing
+      id-token: write
+    steps:
+      # retrieve your distributions here
+      - name: Download from CI runner
+        uses: actions/download-artifact@v4
+        with:
+          name: built-package
+          path: dist/
+      - name: Publish on PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          repository-url: https://test.pypi.org/legacy/

.github/workflows/testpypi.yml

@@ -2,6 +2,46 @@
 
 All notable changes to this project will be documented in this file.
 
+## [1.3.4] - 2025-05-27
+
+### Bug Fixes
+
+- Don't use `or` when param may be 0.\
+  Since Python's expression `a = b or c` will assign `c` to `a` as soon as
+  `b` is "falsy", e.g. also when `b = 0.0`, I should not use this to check
+  if a parameter in the model is `None`.
+
+### Documentation
+
+- Fix misspelled repo link.
+- Remove empty mixins page.
+- Better reuse of README.
+- Move social card to repo root.\
+  This is actually for LyProX: I want to display the social card of all
+  repos in the lycosystem on LyProX's landing page. Therefore, they all
+  need to be in their expected places.
+
+### Miscellaneous Tasks
+
+- Add year range to license.
+
+### Testing
+
+- Use val != 0.5 to test matrix deletion.\
+  0.5 is the new initial value for most parameters, so it does not make
+  sense to use this to check if upon changing a parameter, the transition
+  matrix gets deleted.
+
+### Change
+
+- Init most params with 0.5 instead of 0.0.\
+  In some cases, initializing with 0.0 may have unintended consequences.
+  E.g., a probability of 0.0 cannot be renormalized.
+
+### Ci
+
+- Use OIDC for publishing.
+
 ## [1.3.3] - 2025-03-11
 
 ### Bug Fixes
@@ -866,6 +906,7 @@ Almost the entire API has changed. I'd therefore recommend to have a look at the
 - fix pyproject.toml typo
 - add pre-commit hook to check commit msg
 
+[1.3.4]: https://github.com/rmnldwg/lymph/compare/1.3.3...1.3.4
 [1.3.3]: https://github.com/rmnldwg/lymph/compare/1.3.2...1.3.3
 [1.3.2]: https://github.com/rmnldwg/lymph/compare/1.3.1...1.3.2
 [1.3.1]: https://github.com/rmnldwg/lymph/compare/1.3.0...1.3.1

CHANGELOG.md

@@ -1,4 +1,4 @@
-Copyright (c) 2020 Roman Ludwig & contributors
+Copyright (c) 2020 - 2025 Roman Ludwig & contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal
@@ -16,4 +16,4 @@ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+SOFTWARE.

LICENSE

@@ -68,34 +68,7 @@ LyProX interface
 
 The above mentioned data can also be explored interactively using our online interface `LyProX <https://lyprox.org>`_ `(GitHub repo) <https://github.com/rmnldwg/lyprox>`_.
 
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+.. SEPARATOR
 
 References
 ==========

README.rst

@@ -7,14 +7,6 @@ Detailed API
 
     graph
     models
-    mixins
     components
     types
     utils
-
-
-Index & search
---------------
-
-*  :ref:`genindex`
-*  :ref:`search`

docs/source/api.rst

@@ -1,11 +1,5 @@
-.. image:: ./_static/github-social-card.png
-    :width: 800 px
-
-.. include:: badges.rst
-
-----
-
-.. include:: explanation.rst
+.. include:: ../../README.rst
+    :end-before: .. SEPARATOR
 
 ----
 
@@ -15,20 +9,13 @@ Documentation
 
 .. toctree::
     :maxdepth: 3
-    :caption: Content
 
     install
     quickstart
     api
     license
 
-
-Index & search
---------------
-
-*  :ref:`genindex`
-*  :ref:`search`
-
 ----
 
-.. include:: refs.rst
+.. include:: ../../README.rst
+    :start-after: .. SEPARATOR

docs/source/badges.rst

@@ -247,7 +247,10 @@ def set_params(self, *args: float, **kwargs: float) -> tuple[float]:
 
         for name, value in self._func.keywords.items():
             first, args = popfirst(args)
-            self._func.keywords[name] = first or kwargs.get(name, value)
+            if first is not None:
+                self._func.keywords[name] = first
+            else:
+                self._func.keywords[name] = kwargs.get(name, value)
             if hasattr(self, "_frozen"):
                 del self._frozen
 

docs/source/explanation.rst

@@ -221,7 +221,7 @@ def __init__(
         self,
         parent: Tumor | LymphNodeLevel,
         child: LymphNodeLevel,
-        spread_prob: float = 0.0,
+        spread_prob: float = 0.5,
         micro_mod: float = 1.0,
     ) -> None:
         """Create a new edge between two nodes.
@@ -362,7 +362,7 @@ def set_micro_mod(self, new_micro_mod: float | None) -> None:
     def get_spread_prob(self) -> float:
         """Return the spread probability."""
         if not hasattr(self, "_spread_prob"):
-            self._spread_prob = 0.0
+            self._spread_prob = 0.5
         return self._spread_prob
 
     def set_spread_prob(self, new_spread_prob: float | None) -> None:
@@ -433,7 +433,7 @@ def set_params(self, *args, **kwargs) -> tuple[float]:
         0.4
         """
         first, args = popfirst(args)
-        value = first or self.get_spread_prob()
+        value = first if first is not None else self.get_spread_prob()
 
         if self.is_growth:
             self.set_spread_prob(kwargs.get("growth", value))
@@ -446,7 +446,7 @@ def set_params(self, *args, **kwargs) -> tuple[float]:
             and not self.is_growth
         ):
             first, args = popfirst(args)
-            value = first or self.get_micro_mod()
+            value = first if first is not None else self.get_micro_mod()
             self.set_micro_mod(kwargs.get("micro", value))
 
         return args

docs/source/index.rst

@@ -147,9 +147,9 @@ def __init__(
             other_children["unknown"] = self.unknown
 
         if use_mixing:
-            self.mixing_param = 0.0
+            self.mixing_param = 0.5
 
-        self.midext_prob = 0.0
+        self.midext_prob = 0.5
 
         diagnosis_times.Composite.__init__(
             self,
@@ -489,7 +489,9 @@ def set_params(
         """
         last_param_idx = self.get_num_dims() - 1
         before, last, after = utils.popat(args, idx=last_param_idx)
-        self.midext_prob = kwargs.get("midext_prob", last) or self.midext_prob
+        if kwargs.get("midext_prob", last) is not None:
+            self.midext_prob = kwargs.get("midext_prob", last)
+
         args = self.set_spread_params(*(before + after), **kwargs)
         return self.set_distribution_params(*args, **kwargs)